LIMS2 LIM zinc finger domain containing 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LIMS2provided by HGNC
Official Full Name: LIM zinc finger domain containing 2provided by HGNC
Primary source: HGNC:HGNC:16084
See related: Ensembl:ENSG00000072163 MIM:607908; AllianceGenome:HGNC:16084
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LGMD2W; PINCH2; MDRCMTT; PINCH-2
Summary: This gene encodes a member of a small family of focal adhesion proteins which interacts with ILK (integrin-linked kinase), a protein which effects protein-protein interactions with the extraceullar matrix. The encoded protein has five LIM domains, each domain forming two zinc fingers, which permit interactions which regulate cell shape and migration. A pseudogene of this gene is located on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
Expression: Broad expression in endometrium (RPKM 24.9), fat (RPKM 20.9) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q14.3

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (127638426..127681786, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (128073680..128117027, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (128396001..128439360, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Fluid shear stress modulates endothelial inflammation by targeting LIMS2.
Title: Fluid shear stress modulates endothelial inflammation by targeting LIMS2.
Mammalian cells have two functional PINCH proteins, PINCH1 and PINCH2. PINCH not only binds to Nck2 and engages in the signaling of growth factor receptors, but also forms a ternary complex with ILK and parvin (IPP complex).
Title: Signaling via PINCH: Functions, binding partners and implications in human diseases.
Data indicate compound heterozygous missense mutations that are predicted to be pathogenic in LIM and senescent cell antigen-like domains 2 protein (LIMS2).
Title: LIMS2 mutations are associated with a novel muscular dystrophy, severe cardiomyopathy and triangular tongues.
Results defined the functional role of copy number variations involving PINCH-2 in cancer progression based on the field cancerization effect; cell migration and invasion through autocrine and paracrine function as part of the field cancerization effect.
Title: PINCH-2 presents functional copy number variation and suppresses migration of colon cancer cells by paracrine activity.
PINCH-2 mRNA is overexpressed in malignant mesothelioma
Title: PINCH-2 expression in cancers involving serosal effusions using quantitative PCR.
Observational study of gene-disease association. (HuGE Navigator)
Title: New genetic associations detected in a host response study to hepatitis B vaccine.
LIMS2 may be useful as a molecular biomarker and a therapeutic target by increasing its expression and activity in gastric cancer
Title: The epigenetic silencing of LIMS2 in gastric cancer and its inhibitory effect on cell migration.
These results identify a novel nuclear and focal adhesion protein that associates with ILK and reveals an important role of PINCH-2 in the regulation of the PINCH-1-ILK interaction, cell shape change, and migration.
Title: Characterization of PINCH-2, a new focal adhesion protein that regulates the PINCH-1-ILK interaction, cell spreading, and migration.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal recessive limb-girdle muscular dystrophy type 2W MedGen: C4225192 OMIM: 616827 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of the rate of cognitive decline in Alzheimer's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-85672 (e-PCR)
- UniSTS:103717

SHGC-24307 (e-PCR)
- UniSTS:69487

RH65992 (e-PCR)
- UniSTS:86427

RH78384 (e-PCR)
- UniSTS:47022

A008U17 (e-PCR)
- UniSTS:26801

RH70603 (e-PCR)
- UniSTS:67509

RH68397 (e-PCR)
- UniSTS:72149

WI-13493 (e-PCR)
- UniSTS:77309

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell-cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell junction organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in cholangiocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in integrin-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cholangiocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of hepatocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of neural precursor cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in neural precursor cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of integrin-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of substrate adhesion-dependent cell spreading	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cell-cell junction	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	TAS Traceable Author Statement more info
located_in focal adhesion	HDA more info	PubMed
is_active_in focal adhesion	IBA Inferred from Biological aspect of Ancestor more info
located_in focal adhesion	IDA Inferred from Direct Assay more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: LIM and senescent cell antigen-like-containing domain protein 2

Names: ILK-binding protein; LIM and senescent cell antigen-like domains 2; LIM-type zinc finger domains 2; particularly interesting new Cys-His protein 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_042235.1 RefSeqGene

Range

11257..48361

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001136037.4 → NP_001129509.2 LIM and senescent cell antigen-like-containing domain protein 2 isoform 1

Status: REVIEWED

Description

Transcript Variant: This transcript represents variant 1 and encodes isoform 1.

Source sequence(s)

AC010976, AC074114, AK022470, AK055363, BC065816, DC356496, DR006887

Consensus CDS

CCDS54396.1

UniProtKB/TrEMBL

B3KNZ3

Related

ENSP00000443794.2, ENST00000545738.6

Conserved Domains (5) summary

cd09331
Location:37 → 95

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:98 → 149

LIM2_PINCH; The second LIM domain of protein PINCH

cd09333
Location:162 → 212

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:218 → 271

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:279 → 332

LIM5_PINCH; The fifth LIM domain of protein PINCH
NM_001161403.3 → NP_001154875.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform 3

See identical proteins and their annotated locations for NP_001154875.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.

Source sequence(s)

AC010976, AC074114, BC065816, DR006887

Consensus CDS

CCDS54395.1

UniProtKB/Swiss-Prot

A6NLH0, B4DMV1, F5H6E6, Q7Z4I2, Q7Z4I6, Q7Z4I7, Q7Z4I8, Q8NFE7, Q9HA13

UniProtKB/TrEMBL

B3KNZ3

Related

ENSP00000347240.4, ENST00000355119.9

Conserved Domains (5) summary

cd09331
Location:15 → 73

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:76 → 127

LIM2_PINCH; The second LIM domain of protein PINCH

cd09333
Location:140 → 190

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:196 → 249

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:257 → 310

LIM5_PINCH; The fifth LIM domain of protein PINCH
NM_001161404.2 → NP_001154876.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform 5

See identical proteins and their annotated locations for NP_001154876.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (5) is shorter than isoform 1.

Source sequence(s)

AC010976, AF527766, DA890151

Consensus CDS

CCDS54394.1

UniProtKB/TrEMBL

B3KNZ3

Related

ENSP00000387002.1, ENST00000410011.5

Conserved Domains (5) summary

cd09331
Location:10 → 68

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:71 → 122

LIM2_PINCH; The second LIM domain of protein PINCH

cd09333
Location:135 → 185

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:191 → 244

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:252 → 305

LIM5_PINCH; The fifth LIM domain of protein PINCH
NM_001256542.2 → NP_001243471.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform 4

See identical proteins and their annotated locations for NP_001243471.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) is shorter at the N-terminus, compared to isoform 1.

Source sequence(s)

AF527770, BX458594, DA848179

Consensus CDS

CCDS58725.1

UniProtKB/TrEMBL

Q7Z4I3

Related

ENSP00000386570.1, ENST00000410038.5

Conserved Domains (3) summary

cd09334
Location:44 → 97

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:105 → 158

LIM5_PINCH; The fifth LIM domain of protein PINCH

cl02475
Location:2 → 38

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
NM_017980.5 → NP_060450.2 LIM and senescent cell antigen-like-containing domain protein 2 isoform 2

See identical proteins and their annotated locations for NP_060450.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is longer than isoform 1.

Source sequence(s)

AC074114, AF527764, AF527765, BP221000

Consensus CDS

CCDS2147.1

UniProtKB/TrEMBL

B3KNZ3

Related

ENSP00000326888.5, ENST00000324938.9

Conserved Domains (5) summary

cd09331
Location:39 → 97

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:100 → 151

LIM2_PINCH; The second LIM domain of protein PINCH

cd09333
Location:164 → 214

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:220 → 273

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:281 → 334

LIM5_PINCH; The fifth LIM domain of protein PINCH

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

127638426..127681786 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006712627.5 → XP_006712690.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X9

UniProtKB/TrEMBL

Q7Z4I3

Conserved Domains (3) summary

cd09333
Location:24 → 74

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:80 → 133

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:141 → 194

LIM5_PINCH; The fifth LIM domain of protein PINCH
XM_005263710.3 → XP_005263767.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X6

UniProtKB/TrEMBL

Q7Z4I5

Conserved Domains (4) summary

cd09332
Location:7 → 58

LIM2_PINCH; The second LIM domain of protein PINCH

cd09333
Location:71 → 121

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:127 → 180

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:188 → 241

LIM5_PINCH; The fifth LIM domain of protein PINCH
XM_047444970.1 → XP_047300926.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X4
XM_024452983.2 → XP_024308751.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X2

UniProtKB/TrEMBL

B3KNZ3

Related

ENSP00000386637.2, ENST00000409808.6

Conserved Domains (5) summary

cd09331
Location:10 → 68

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:71 → 122

LIM2_PINCH; The second LIM domain of protein PINCH

cd09333
Location:135 → 185

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:191 → 244

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:252 → 305

LIM5_PINCH; The fifth LIM domain of protein PINCH
XM_011511453.2 → XP_011509755.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X3

Conserved Domains (4) summary

cd09331
Location:39 → 97

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:100 → 151

LIM2_PINCH; The second LIM domain of protein PINCH

cd09335
Location:240 → 293

LIM5_PINCH; The fifth LIM domain of protein PINCH

cl02475
Location:164 → 205

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
XM_047444963.1 → XP_047300919.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X1
XM_024452986.2 → XP_024308754.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X11

UniProtKB/TrEMBL

Q7Z4I3

Related

ENSP00000386252.1, ENST00000409286.5

Conserved Domains (3) summary

cd09334
Location:44 → 97

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:105 → 158

LIM5_PINCH; The fifth LIM domain of protein PINCH

cl02475
Location:2 → 38

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
XM_047444976.1 → XP_047300932.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X11
XM_047444975.1 → XP_047300931.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X11
XM_024452985.2 → XP_024308753.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X11

UniProtKB/TrEMBL

Q7Z4I3

Conserved Domains (3) summary

cd09334
Location:44 → 97

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:105 → 158

LIM5_PINCH; The fifth LIM domain of protein PINCH

cl02475
Location:2 → 38

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
XM_047444972.1 → XP_047300928.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X7
XM_017004469.2 → XP_016859958.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X8
XM_047444971.1 → XP_047300927.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X5
XM_006712628.4 → XP_006712691.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X10

Conserved Domains (2) summary

cd09331
Location:39 → 97

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:100 → 143

LIM2_PINCH; The second LIM domain of protein PINCH

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

128073680..128117027 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054342902.1 → XP_054198877.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X9
XM_054342899.1 → XP_054198874.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X6
XM_054342897.1 → XP_054198872.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X4
XM_054342895.1 → XP_054198870.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X2
XM_054342896.1 → XP_054198871.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X3
XM_054342894.1 → XP_054198869.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X1
XM_054342905.1 → XP_054198880.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X11
XM_054342904.1 → XP_054198879.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X11
XM_054342900.1 → XP_054198875.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X7
XM_054342901.1 → XP_054198876.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X8
XM_054342898.1 → XP_054198873.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X5
XM_054342903.1 → XP_054198878.1 LIM and senescent cell antigen-like-containing domain protein 2 isoform X10